1 Overview of GAGA assemblies

1.1 Taxon sampling

We so far have genomic data for 162 species distributed across the 347 genera of ants (Fig 1.1), covering 27 tribes in 12 subfamilies.

Ant genera targeted so far by GAGA

Figure 1.1: Ant genera targeted so far by GAGA

1.2 Sequencing techniques

Most (n= 124) of the species have been sequenced with PacBio, while some rare species (e.g. Leptanilla) could only be sequenced with stLFR (n= 20), commonly due to lack of sufficient biomass (Fig. 1.2). HiC sequencing was so far done for 10 species.
Sequencing techniques for different species

Figure 1.2: Sequencing techniques for different species

1.3 Genome completeness

Most genomes reach high BUSCO scores (Fig 1.3), both against Hymenoptera (median 97 %) and Eukaryota (median 98 %). A few stLFR-only genomes however are incomplete with BUSCO scores as low as ~70 % (e.g. Gigantiops destructor with 68.3 % complete Hymenoptera BUSCOs).

Complete BUSCOs in different species

Figure 1.3: Complete BUSCOs in different species

1.4 Genome sizes of all so far sequenced species

The assembled genomes vary considerably in size, ranging from 189 MB (Myrmecia croslandi 2n=2) to 594 MB (Odontomachus cf. monticola). Overall, genome size tends to vary most in the Ponerinae and least in the Formicinae. Figure 1.4 gives a complete overview of all so far sequenced species and the respective genome assembly size in Mb.

Figure 1.4: Genome sizes of GAGA genome assemblies

1.5 Preliminary quality of the assembled genomes

Our sequencing strategy has evolved further, now combining long-read PacBio data, linked-short-read stLFR data and if possible HiC data. We expect that together, these data will yield highly contiguous high quality genome assemblies that should be close to chromosome-resolution for most of the species.

Figure 1.5 gives a rough overview of the quality of the genome assemblies we have so far.

Figure 1.5: Genome assembly quality for GAGA species.

On average, scaffold N50 is 4.505 mega bases (Mb) Currently, the species with the highest scaffold N50 is Plagiolepis pygmaea with 32.91 MB.

Genome assembly quality overview for GAGA species.

Figure 1.6: Genome assembly quality overview for GAGA species.

1.6 Overview Table

Table 1.1 gives an overview of all so far sequenced species.
Table 1.1: Overview of sequenced species
GAGA-id Taxon Tribe Subfamily Sequencing Technique Genome Size %BUSCO (Hym) %BUSCO (Euk) N50scf Assembly Status
GAGA-0392 Leptanilla sp. Leptanillini Leptanillinae stLFR 224 93.3 98.0 0.13 Final
GAGA-0580 Probolomyrmex longiscapus Probolomyrmecini Proceratiinae stLFR 316 79.8 87.9 0.86 Final
GAGA-0535 Discothyrea kamiteta Proceratiini Proceratiinae stLFR 233 84.1 91.8 0.02 Final
GAGA-0389 Proceratium itoi Proceratiini Proceratiinae stLFR 308 81.7 87.9 0.02 Final
GAGA-0537 Proceratium cf. bruelheidei Proceratiini Proceratiinae stLFR 308 83.0 86.7 0.02 Final
GAGA-0536 Prionopelta kraepelini Amblyoponini Amblyoponinae stLFR 243 75.6 79.6 0.05 Final
GAGA-0391 Stigmatomma cf. rubiginoum Amblyoponini Amblyoponinae P/s 286 95.1 96.9 5.42 Final
GAGA-0404 Mystrium cf. camillae Amblyoponini Amblyoponinae P/s 290 96.2 95.6 6.05 Final
GAGA-0090 Platythyrea punctata Platythyreini Ponerinae P/s 196 96.4 98.1 4.49 Final
GAGA-0063 Neoponera goeldii Ponerini Ponerinae P/s 554 95.6 98.0 8.32 Final
NCBI-0007 Dinoponera quadriceps Ponerini Ponerinae non-GAGA 258 96.3 97.3 1.36 NCBI assembly
GAGA-0083 Diacamma cf. indicum Ponerini Ponerinae P/s 233 93.0 93.4 17.25 Final
GAGA-0351 Diacamma rugosum Ponerini Ponerinae P/s 269 96.5 98.8 7.84 Final
GAGA-0266 Ectomomyrmex cf. javanus sp2 Ponerini Ponerinae P/s 434 93.4 96.5 0.81 Final
GAGA-0300 Ectomomyrmex javanus Ponerini Ponerinae P/s 470 95.8 98.5 1.82 Final
GAGA-0303 Harpegnathos venator Ponerini Ponerinae P/s 324 97.2 98.5 3.00 Final
NCBI-0009 Harpegnathos saltator Ponerini Ponerinae non-GAGA 335 97.3 98.1 1.08 NCBI assembly
GAGA-0307 Hypoponera opacior Ponerini Ponerinae P/s 251 97.0 98.5 6.95 Final
GAGA-0352 Leptogenys diminuta Ponerini Ponerinae P/s 348 97.1 97.3 9.63 Final
GAGA-0380 Leptogenys cf. kitteli Ponerini Ponerinae P/s 318 97.1 98.5 6.35 Final
GAGA-0387 Leptogenys cf. binghamii Ponerini Ponerinae stLFR 265 89.3 90.6 0.08 Final
GAGA-0408 Buniapone amblyops Ponerini Ponerinae stLFR 306 94.3 98.1 0.12 Final
GAGA-0246 Pseudoneoponera rufipes Ponerini Ponerinae P/s 305 96.8 97.7 7.76 Final
GAGA-0386 Euponera pilosior Ponerini Ponerinae stLFR 397 84.2 96.5 0.05 Final
GAGA-0301 Anochetus risii Ponerini Ponerinae P/s 438 94.5 96.9 4.72 Final
GAGA-0074 Odontomachus hastatus Ponerini Ponerinae P/s 412 96.4 99.2 3.13 Final
GAGA-0353 Odontomachus cf. monticola Ponerini Ponerinae P/s 594 95.5 97.3 2.69 Final
NCBI-0011 Odontomachus brunneus Ponerini Ponerinae non-GAGA 393 96.5 98.9 1.76 NCBI assembly
GAGA-0025 Megaponera analis Ponerini Ponerinae P/s 312 96.4 98.1 6.45 Final
GAGA-0552 Paraponera clavata tr. Paraponerinae Paraponerinae P/s 227 96.2 95.6 6.18 Final
GAGA-0379 Cerapachys sulcinodis tr. Dorylinae Dorylinae P/s 315 96.8 97.7 2.37 Final
NCBI-0001 Ooceraea biroi tr. Dorylinae Dorylinae non-GAGA 224 97.4 97.7 16.89 NCBI assembly
GAGA-0534 Dorylus orientalis tr. Dorylinae Dorylinae P/s 190 96.3 98.4 14.28 Final
GAGA-0577 Parasyscia sp. tr. Dorylinae Dorylinae stLFR 241 78.6 87.5 0.02 Final
GAGA-0517 Myrmecia pilosula Myrmeciini Myrmeciinae P/s 219 98.1 98.1 11.50 Final
GAGA-0521 Myrmecia croslandi 2n=2 Myrmeciini Myrmeciinae P/s 189 96.6 96.1 26.09 Final, but will be Hi-C scaffolded
GAGA-0522 Myrmecia croslandi 2n=4 Myrmeciini Myrmeciinae P/s 196 98.1 98.8 21.92 Final
GAGA-0365 Tetraponera rufonigra tr. Pseudomyrmecinae Pseudomyrmecinae P/s 251 95.3 98.1 9.03 Final
GAGA-0343 Pseudomyrmex spinicola tr. Pseudomyrmecinae Pseudomyrmecinae P/s 263 96.9 98.1 4.52 Final
GAGA-0528 Liometopum microcephalum Tapinomini Dolichoderinae P/s 230 96.3 96.4 1.22 Final
GAGA-0337 Tapinoma melanocephalum Tapinomini Dolichoderinae P/s 255 95.4 97.6 6.18 Final
GAGA-0340 Tapinoma cf. melanocephalum Tapinomini Dolichoderinae P/s 261 94.6 96.1 9.68 Final
NCBI-0010 Linepithema humile Leptomyrmecini Dolichoderinae non-GAGA 219 97.2 98.9 1.40 NCBI assembly
GAGA-0302 Ochetellus glaber Leptomyrmecini Dolichoderinae P/s 300 96.2 97.3 3.64 Final
GAGA-0363 Iridomyrmex anceps Leptomyrmecini Dolichoderinae P/s 224 95.7 96.1 9.59 Final
GAGA-0020 Lasius flavus sp.2 Lasiini Formicinae P/H 320 95.2 95.7 5.72 Final
GAGA-0024 Lasius flavus Lasiini Formicinae P/H/s 300 97.6 98.8 18.92 Final
GAGA-0177 Lasius niger Lasiini Formicinae P/H/s 287 96.9 96.5 19.67 Final
GAGA-0364 Lasius sp1 Lasiini Formicinae P/s 251 98.0 99.6 3.58 Final, validating species ID (Paco)
GAGA-0366 Lasius neglectus Lasiini Formicinae stLFR 255 92.7 97.3 0.03 Final
GAGA-0491 Lasius fuliginosus Lasiini Formicinae P/s 240 97.7 99.2 2.37 Final
GAGA-0524 Lasius fuliginosus Lasiini Formicinae P/s 239 97.9 99.2 1.65 Final
GAGA-0532 Lasius alienus Lasiini Formicinae P/s 287 97.8 98.8 3.29 Final
GAGA-0026 Myrmecocystus cf. mendax Lasiini Formicinae P/H 220 98.1 99.2 14.29 Final
GAGA-0341 Nylanderia fulva Lasiini Formicinae PacBio 337 97.1 98.8 2.58 Final
GAGA-0332 Pseudolasius sp. Lasiini Formicinae P/s 265 95.8 96.9 4.62 Final
GAGA-0275 Euprenolepis cf wittei Lasiini Formicinae P/s 266 97.7 99.2 2.38 Final
GAGA-0350 Formica fusca Formicini Formicinae P/s 333 95.2 94.5 2.18 Final
GAGA-0359 Formica cf. japonica Formicini Formicinae P/s 389 96.6 97.6 1.78 Final
GAGA-0485 Formica sanguinea Formicini Formicinae P/s 348 97.6 99.6 3.98 Final
GAGA-0495 Formica fusca Formicini Formicinae stLFR 246 94.4 97.7 0.13 Final
NCBI-0008 Formica exsecta Formicini Formicinae non-GAGA 275 96.2 98.4 1.01 NCBI assembly
OUT-0001 Formica selysi Formicini Formicinae non-GAGA 290 96.9 98.0 7.92 NCBI assembly
OUT-0002 Formica cinerea Formicini Formicinae PacBio 324 98.2 98.9 5.06 Final
GAGA-0502 Iberoformica subrufa Formicini Formicinae P/s 290 97.9 97.7 4.81 Final
GAGA-0304 Proformica cf. mongolica Formicini Formicinae P/s 257 95.4 94.9 4.70 Final
GAGA-0354 Cataglyphis aenescens Formicini Formicinae P/s 279 97.7 98.4 5.34 Final
GAGA-0334 Rossomyrmex quandratinodum Formicini Formicinae P/s 251 97.5 98.8 5.05 Final
GAGA-0494 Rossomyrmex minuchae Formicini Formicinae P/s 253 97.0 97.7 5.31 Final
GAGA-0336 Oecophylla smaragdina Oecophyllini Formicinae P/s 219 97.5 98.8 7.71 Final
GAGA-0199 Anoplolepis gracilipes Plagiolepidini Formicinae P/s 253 98.1 99.2 9.15 Final
GAGA-0338 Lepisiota rothneyi Plagiolepidini Formicinae P/s 351 96.7 97.7 2.55 Final
GAGA-0187 Plagiolepis pygmaea Plagiolepidini Formicinae P/H/s 335 96.6 97.7 32.91 Final
GAGA-0055 Gigantiops destructor Gigantiopini Formicinae stLFR 241 68.3 82.8 0.01 Final
GAGA-0406 Myrmoteras binghamii Myrmoteratini Formicinae stLFR 283 73.0 88.3 0.01 Final
GAGA-0360 Colobopsis sp. Camponotini Formicinae P/s 262 98.3 99.2 9.35 Final
GAGA-0374 Polyrhachis illaudata Camponotini Formicinae P/s 274 97.8 96.9 2.41 Final
GAGA-0200 Camponotus japonicus Camponotini Formicinae P/s 306 98.0 97.7 1.49 Final
GAGA-0221 Camponotus fellah Camponotini Formicinae P/H/s 278 98.0 98.4 12.30 Final
GAGA-0361 Camponotus cf. fedtschenkoi Camponotini Formicinae P/s 252 98.0 98.0 9.40 Final
GAGA-0362 Camponotus sp. Camponotini Formicinae P/s 284 97.8 99.2 8.31 Final
GAGA-0396 Camponotus singularis Camponotini Formicinae P/s 264 98.0 98.4 3.46 Final
NCBI-0005 Camponotus floridanus Camponotini Formicinae non-GAGA 284 98.5 98.4 1.59 NCBI assembly
GAGA-0028 Myrmica rubra Myrmicini Myrmicinae P/s 477 95.2 97.3 1.45 Final
GAGA-0087 Myrmica scabrinodis Myrmicini Myrmicinae P/s 478 97.0 98.9 1.66 Final
GAGA-0401 Myrmica sp. Myrmicini Myrmicinae P/s 474 96.5 97.7 0.71 Final
GAGA-0114 Manica rubida Myrmicini Myrmicinae P/H/s 331 95.5 98.9 11.52 Final
NCBI-0012 Pogonomyrmex barbatus Pogonomyrmecini Myrmicinae non-GAGA 236 93.4 95.7 0.82 NCBI assembly
GAGA-0109 Stenamma debile Stenammini Myrmicinae P/s 380 96.4 95.7 2.10 Final
GAGA-0084 Aphaenogaster subterranea Stenammini Myrmicinae P/s 415 97.4 98.1 6.51 Final
GAGA-0356 Aphaenogaster exasperata Stenammini Myrmicinae P/s 398 98.0 98.4 4.32 Final
GAGA-0531 Aphaenogaster famelica Stenammini Myrmicinae P/s 369 96.8 96.1 1.63 Final
GAGA-0004 Messor barbarus Stenammini Myrmicinae P/s 313 97.5 98.4 9.08 Final
GAGA-0413 Messor capitatus Stenammini Myrmicinae P/s 305 98.3 98.4 11.42 Final
GAGA-0505 Goniomma hispanicum Stenammini Myrmicinae P/s 290 98.2 98.5 13.80 Final
GAGA-0503 Oxyopomyrmex saulcyi Stenammini Myrmicinae P/s 274 98.3 98.8 10.82 Final
GAGA-0454 Solenopsis fugax Solenopsidini Myrmicinae P/s 383 97.3 98.4 2.83 Final
NCBI-0002 Solenopsis invicta Solenopsidini Myrmicinae non-GAGA 414 98.0 98.8 13.11 NCBI assembly
GAGA-0245 Monomorium pharaonis Solenopsidini Myrmicinae P/H/s 326 97.8 99.2 29.66 Final, Chr-level
GAGA-0346 Megalomyrmex milenae Solenopsidini Myrmicinae P/H/s 352 97.3 98.0 10.85 Final
NCBI-0014 Wasmannia auropunctata Attini Myrmicinae non-GAGA 306 96.6 98.1 1.42 NCBI assembly
GAGA-0540 Myrmicocrypta uncinata Attini Myrmicinae P/s 441 95.8 95.6 1.90 Final
GAGA-0543 Kalathomyrmex emeryi Attini Myrmicinae P/s 299 97.4 98.0 6.55 Final
GAGA-0541 Mycetosoritis hartmanni Attini Myrmicinae P/s 349 94.8 96.1 4.66 Final
NCBI-0006 Cyphomyrmex costatus Attini Myrmicinae non-GAGA 297 97.8 99.6 1.17 NCBI assembly
GAGA-0539 Mycetophylax morschi Attini Myrmicinae P/s 309 98.1 98.4 7.84 Final
GAGA-0538 Sericomyrmex mayri Attini Myrmicinae P/s 396 97.9 98.1 5.32 Final
GAGA-0550 Xerolitor explicatus Attini Myrmicinae P/s 469 94.6 96.5 0.85 Final
NCBI-0015 Trachymyrmex zeteki Attini Myrmicinae non-GAGA 267 97.5 98.0 1.33 NCBI assembly
NCBI-0016 Trachymyrmex septentrionalis Attini Myrmicinae non-GAGA 290 98.0 98.8 2.52 NCBI assembly
NCBI-0017 Trachymyrmex cornetzi Attini Myrmicinae non-GAGA 365 97.2 98.4 0.78 NCBI assembly
GAGA-0001 Acromyrmex ameliae Attini Myrmicinae P/s 290 96.4 98.0 8.21 Final
GAGA-0002 Acromyrmex subterraneus Attini Myrmicinae stLFR 318 80.1 89.8 0.09 Final
GAGA-0003 Acromyrmex lobicornis Attini Myrmicinae P/H 335 98.4 98.8 17.01 Final
GAGA-0014 Acromyrmex echinatior Attini Myrmicinae PacBio 296 97.2 98.1 8.27 Final
GAGA-0220 Acromyrmex octospinosus Attini Myrmicinae stLFR 315 86.1 89.0 0.30 Final
NCBI-0003 Atta cephalotes Attini Myrmicinae non-GAGA 318 93.4 97.3 5.15 NCBI assembly
NCBI-0004 Atta colombica Attini Myrmicinae non-GAGA 291 98.1 98.8 2.04 NCBI assembly
GAGA-0080 Pheidole pallidula Attini Myrmicinae PacBio 302 97.9 98.9 4.67 Final
GAGA-0358 Pheidole nodus Attini Myrmicinae P/s 347 97.0 97.3 5.82 Final
GAGA-0376 Pheidole capellinii Attini Myrmicinae P/s 293 95.9 97.3 5.23 Final
GAGA-0384 Pheidole selathorax Attini Myrmicinae P/s 275 95.1 94.6 5.30 Final
GAGA-0530 Pheidole yeensis Attini Myrmicinae P/s 327 97.7 99.2 3.35 Final
GAGA-0229 Cephalotes cf minutus Attini Myrmicinae P/s 408 96.2 98.1 2.79 Final
GAGA-0554 Strumigenys mutica Attini Myrmicinae stLFR 233 92.6 96.5 0.06 Final
GAGA-0515 Cardiocondyla obscurior Crematogastrini Myrmicinae PacBio 189 98.7 98.9 5.74 Final
GAGA-0328 Carebara diversa Crematogastrini Myrmicinae P/s 200 98.4 99.2 4.85 Final
GAGA-0331 Carebara sp. s2 Crematogastrini Myrmicinae stLFR 214 85.5 93.0 0.04 Final
GAGA-0378 Carebara bengalensis Crematogastrini Myrmicinae PacBio 209 95.7 95.7 6.15 Final
GAGA-0382 Carebara trechideros Crematogastrini Myrmicinae P/s 201 98.5 99.6 8.19 Final
GAGA-0533 Carebara sp. Crematogastrini Myrmicinae P/s 194 98.5 99.6 7.60 Final
GAGA-0578 Carebara capreola Crematogastrini Myrmicinae PacBio 229 96.4 96.5 5.07 Final
GAGA-0579 Carebara melasolena Crematogastrini Myrmicinae PacBio 202 97.6 98.9 5.22 Final
GAGA-0520 Melissotarsus emeryi Crematogastrini Myrmicinae P/s 387 95.6 97.7 6.49 Final
GAGA-0085 Tetramorium caespitum Crematogastrini Myrmicinae P/s 258 96.5 96.9 8.26 Final
GAGA-0333 Tetramorium bicarinatum Crematogastrini Myrmicinae P/s 261 97.6 98.8 11.33 Final
GAGA-0405 Tetramorium sp. Crematogastrini Myrmicinae P/s 262 97.3 99.2 5.15 Final
GAGA-0527 Tetramorium “Anergates” atratulus Crematogastrini Myrmicinae P/s 215 96.7 98.8 11.76 Final
GAGA-0553 Tetramorium sp. Crematogastrini Myrmicinae stLFR 238 87.1 95.3 0.03 Final
NCBI-0013 Vollenhovia emeryi Crematogastrini Myrmicinae non-GAGA 287 97.5 98.5 1.35 NCBI assembly
GAGA-0330 Crematogaster cf. rogenhoferi Crematogastrini Myrmicinae P/s 365 97.5 97.3 2.29 Final
GAGA-0393 Crematogaster cf. osakensis Crematogastrini Myrmicinae P/s 263 96.9 97.3 4.28 Final
GAGA-0395 Crematogaster osakensis Crematogastrini Myrmicinae P/s 266 96.5 96.1 5.67 Final
GAGA-0335 Meranoplus cf. bicolor Crematogastrini Myrmicinae P/s 254 97.3 98.1 5.87 Final
GAGA-0165 Eutetramorium mocquerysi Crematogastrini Myrmicinae P/s 237 98.4 99.3 9.23 Final, additional pacbio data
GAGA-0407 Kartidris sp. Crematogastrini Myrmicinae P/s 238 96.4 96.9 6.19 Final
GAGA-0256 Acanthomyrmex ferox Crematogastrini Myrmicinae P/s 293 96.9 96.9 2.52 Final
GAGA-0103 Myrmecina graminicola Crematogastrini Myrmicinae P/s 309 95.8 96.9 1.46 Final
GAGA-0082 Pristomyrmex punctatus Crematogastrini Myrmicinae P/s 291 96.2 98.0 8.36 Final
GAGA-0222 Temnothorax rugatulus Crematogastrini Myrmicinae PacBio 322 95.2 97.3 1.99 Final
GAGA-0223 Temnothorax longispinosus Crematogastrini Myrmicinae PacBio 302 95.4 96.5 1.18 Final
GAGA-0224 Temnothorax americanus Crematogastrini Myrmicinae PacBio 256 96.2 97.7 3.89 Final
GAGA-0288 Temnothorax unifasciatus Crematogastrini Myrmicinae PacBio 287 95.5 95.7 2.09 Final
GAGA-0510 Temnothorax nylanderi Crematogastrini Myrmicinae PacBio 293 95.2 97.3 2.16 Final
GAGA-0511 Temnothorax ravouxi Crematogastrini Myrmicinae PacBio 371 94.6 95.7 0.62 Final
GAGA-0512 Temnothorax pilagens Crematogastrini Myrmicinae PacBio 310 96.0 98.1 1.98 Final
GAGA-0513 Temnothorax ambiguus Crematogastrini Myrmicinae PacBio 303 96.0 97.7 2.33 Final
GAGA-0098 Harpagoxenus sublaevis Crematogastrini Myrmicinae PacBio 313 95.4 96.1 2.52 Final
GAGA-0463 Formicoxenus nitidulus Crematogastrini Myrmicinae P/s 307 97.4 98.4 4.55 Final
GAGA-0099 Leptothorax acervorum Crematogastrini Myrmicinae PacBio 342 95.0 97.3 2.02 Final
GAGA-0306 Gnamptogenys bicolor Ectatommini Ectatomminae P/s 320 96.1 97.3 5.06 Final
GAGA-0234 Typhlomyrmex rogenhoferi Typhlomyrmecini Ectatomminae stLFR 377 91.3 94.5 0.08 Final